Genomic Analysis of Cutibacterium acnes Strains Isolated from Prosthetic Joint Infections
Abstract
:1. Introduction
2. Materials and Methods
2.1. Strain Isolation and Growth Conditions
2.2. DNA Isolation and Genome Sequencing
2.3. Bioinformatics Tools and Analyses
3. Results
3.1. Strain Cohort
3.2. Typing and Whole Genome Phylogeny of C. acnes Strains
3.3. Genomic Differences beyond the Phylotype Level Due to the Presence of a Plasmid
3.4. Genomic Differences beyond the Phylotype Level Due to Other Genomic Islands
4. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Strain | GenBank | Source | Joint Site | Phylotype | SLST | Size (bp) | Coverage | Contigs | N50 (bp) | Plasmid | Geographical Origin |
---|---|---|---|---|---|---|---|---|---|---|---|
ZH7 | JAGDNT000000000 | Relapse PJI | Hip | IB | H1 | 2,544,272 | 203 | 17 | 323,469 | - | Zürich, Switzerland |
P8 | JAGDNS000000000 | Relapse PJI | Shoulder | IB | H1 | 2,545,631 | 169 | 19 | 168,849 | - | Paris, France |
P15 | JAGDNR000000000 | Relapse PJI | Hip | IB | H1 | 2,544,110 | 193 | 16 | 572,713 | - | Paris, France |
P31 | JAGDNQ000000000 | Relapse PJI | Shoulder | IA | F4 | 2,482,181 | 171 | 14 | 690,112 | - | Paris, France |
S2 | JAGDNP000000000 | Relapse PJI | Hip | IB | H1 | 2,545,388 | 183 | 19 | 337,942 | - | Santander, Spain |
HOL1 | JAGDNO000000000 | Relapse PJI | Shoulder | IA | D1 | 2,535,867 | 178 | 16 | 738,597 | - | Groningen, Netherlands |
261 | JAGDNN000000000 | PJI | Shoulder | IB | H1 | 2,604,163 | 133 | 25 | 323,553 | 54.2 | Madrid, Spain |
ZH8 | JAGDNM000000000 | PJI | Hip | IA | C1 | 2,526,283 | 187 | 20 | 302,006 | 46.1 | Zürich, Switzerland |
S3 | JAGDNL000000000 | PJI | Shoulder | II | Knew | 2,478,438 | 207 | 9 | 725,650 | - | Santander, Spain |
P38 | JAGDNK000000000 | PJI | Shoulder | II | K1 | 2,459,078 | 135 | 12 | 523,312 | - | Paris, France |
ESL8 | JAGDNJ000000000 | PJI | Knee | IA | A1 | 2,579,590 | 133 | 22 | 400,190 | 54.0 | Ankaran, Slovenia |
N5 | JAGDNI000000000 | PJI | Shoulder | IA | A1 | 2,478,335 | 168 | 14 | 344,049 | - | Nantes, France |
HS14 | JAGDNH000000000 | Skin | - | IA | D1 | 2,536,118 | 187 | 10 | 738,783 | - | Madrid, Spain |
HS18 | JAGDNG000000000 | Skin | - | IA | D1 | 2,535,241 | 213 | 14 | 700,603 | - | Madrid, Spain |
HS29 | JAGDNF000000000 | Skin | - | IA | F4 | 2,543,557 | 160 | 24 | 280,277 | 52.6 | Madrid, Spain |
HS50 | JAGDNE000000000 | Skin | - | IA | A1 | 2,479,007 | 163 | 10 | 738,366 | - | Madrid, Spain |
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Salar-Vidal, L.; Achermann, Y.; Aguilera-Correa, J.-J.; Poehlein, A.; Esteban, J.; Brüggemann, H.; on behalf of the ESCMID Study Group for Implant-Associated Infections (ESGIAI). Genomic Analysis of Cutibacterium acnes Strains Isolated from Prosthetic Joint Infections. Microorganisms 2021, 9, 1500. https://doi.org/10.3390/microorganisms9071500
Salar-Vidal L, Achermann Y, Aguilera-Correa J-J, Poehlein A, Esteban J, Brüggemann H, on behalf of the ESCMID Study Group for Implant-Associated Infections (ESGIAI). Genomic Analysis of Cutibacterium acnes Strains Isolated from Prosthetic Joint Infections. Microorganisms. 2021; 9(7):1500. https://doi.org/10.3390/microorganisms9071500
Chicago/Turabian StyleSalar-Vidal, Llanos, Yvonne Achermann, John-Jairo Aguilera-Correa, Anja Poehlein, Jaime Esteban, Holger Brüggemann, and on behalf of the ESCMID Study Group for Implant-Associated Infections (ESGIAI). 2021. "Genomic Analysis of Cutibacterium acnes Strains Isolated from Prosthetic Joint Infections" Microorganisms 9, no. 7: 1500. https://doi.org/10.3390/microorganisms9071500
APA StyleSalar-Vidal, L., Achermann, Y., Aguilera-Correa, J. -J., Poehlein, A., Esteban, J., Brüggemann, H., & on behalf of the ESCMID Study Group for Implant-Associated Infections (ESGIAI). (2021). Genomic Analysis of Cutibacterium acnes Strains Isolated from Prosthetic Joint Infections. Microorganisms, 9(7), 1500. https://doi.org/10.3390/microorganisms9071500